Ann Taylor Sandbox 118

Thrombin
Thrombin is a "trypsin-like" serine protease. Its structure (PDB code 1ppb) is shown here with a peptide chloroketone inhibitor (PPACK). The thrombin A chain (cleaved N terminal fragement) is shown in cyan and the B chain is shown in red. The Active site is made up of a catalytic triad of Ser195, His57 and Asp102, backed up by Ser214. The peptide chloroketone inhibitor (PPACK) is shown in purple. A closeup shows the activation site at which the sidechain of Asp194 makes a salt link with the N-terminus at residue 16, newly formed when the A chain is cleaved in the zymogen-to-enzyme activation process. The specificity pocket is on one side of the throat of the domain 2 beta barrel, and the activation site is close next to it.

The B chain consists of two domains. As is true for all of the "trypsin-like" serine proteases, each of the two thrombin domains consists mainly of a 6-stranded, antiparallel beta barrel. The specificity pocket (here filled with the Lys sidechain of the PPACK inhibitor) is in one side of the throat of the domain 2beta barrel, and the activation site is close next to it.



Trypsin-BPTI complex
The trypsin backbone is shown in pink and the trypsin inhibitor, BPTI, in yellow (PDB code 2ptc). The active site residues [Ser195-His57-Asp102-Ser214] are shown in green, the disulfide bond between residues 14-38 is shown in yellow and the Lys 15 sidechain at the specificity site in pink.

Gilman-Cassady suc-AAPK-trypsin
suc-AAPK-trypsin is a serine protease in the acyl-enzyme state. The significant protease structure is composed of Ser 195, His 57, and Aspartate 102, which combine to form the Catalytic Triad. Koshland et. al. (2006) show that suc-AAPK-trypsin binds substrate between Ser 195 and His 57 in the serine protease mechanism. This substrate is said to have two orientations, the first orientation is His 57 directly interacting with Ser 195 allowing H-bond stablization. The second orientation shows His 57 rotated around its C-alpha and C-beta bonds in which it is out of the reach of H-bond stabalization. Throughout the serine protease mechanism Hydrogen bonding is an important stabalizing function, for example the oxyanion hole is a stablization of two amide hydrogens bonding to an oxygen. For this reason, a possible function of the second conformation could be for stabilzing the molecule for such things as ligand binding.